I am not sure that I understand the infection or hyperfiltration theories in your case but the rest is plausible. I would ask your urologist to evaluate you for RTA (renal tubular acidosis) which will require some blood work. Actually a stone workup involves both blood and urine tests. The blood at least for: uric acid, electrolytes( sodium, potassium, chloride, hco2), creatinine, phosphorus, calcium and the urine at least for: uric acid, magnesium, calcium, citrate, oxalate, creatinine and sodium.
I would suggest a yearly x-ray of your abdomen (not a CAT scan) to observe any remaining stones for growth. The blood in your urine may occur from time to time because of the existence of the stones, If you have not had a cystoscopy to look for causes of blood in your urine from something other than stones, then I would recommend a cystoscopy.
Stones that are not causing obstruction and are not infected should not be causing pain. I think that those episodes of pain and hematuria are likely related to the passage of small stones.
Can you be rendered stone free? I cannot tell. In part this answer would be related to the cause of your stones. Certainly, I think that we can find medication and/or diet to decrease the recurrence rate of stones and keep any that are in your kidneys from growing.
Hope this helps.
Just adding more detail to my initial question. I received my surgery report and it states that the remaining stones are in the intraparenchymal region of the kidney. It also states that the upper most calix, middle calices and the lower calix all have intraparenchymal stones and Randall plaques. But, the Randall plaques were removed.